No description available.

No description available.

A 5' AMP-degrading activity appears during the course of development in Dictyostelium discoideum between the prestalk and prespore zones. This enzyme is referred as 5'-Nucleotidase (5NT). Given the critical role of cyclic AMP in cell differentiation in this organism, 5NT is thought to be involved in cell positioning during development. Southern blot analysis showed a single form of the gene. The expression of the 5nt gene is known to be developmentally regulated. The message appears first at about 5 hr of the Dictyostelium development and remains constant throughout the rest of the development. Primer extension indicated two potential transcriptional start sites (118 bp and 148 bp upstream of the ATG initiation codon) for the 5nt expression. The 5nt promoter region was cloned and analyzed to investigate the expression of 5nt. Analysis of the cloned 5nt promoter fused to lacZ enabled the localization of the 5nt expression in pstAB cells during development. To identify cis-acting regulatory sequences, a series of 5' and internal promoter deletions were generated and fused to a luciferase reporter gene. The reporter activity driven by the 1,212 bp promoter started at the early aggregation stage, in agreement with temporal expression of the 5nt gene. Also, the expression was induced by exogenous cAMP. The reporter activity was high and relatively equivalent for all deletion constructs that contained 547 bp or more of the promoter region. No luciferase activity was detected using 365 bp or less of the promoter. A gradual decrease in activity was observed when three deletion constructs between -547 and -365 bp were tested suggesting the presence of at least two cis-regulatory elements within this region. Internal deletion analysis indicated another potential regulatory region located between -307 and -226 bp. To identify protein factor(s) that bind specifically to these regulatory sequences, gel shift assays were performed. Two bands, 0.33 Rf and 0.13 Rf, were detected in both cytoplasmic and nuclear extracts using radiolabeled DNA fragments located between -227 and -198 bp and -252 and -203 bp of the promoter region, respectively. Competition experiments confirmed the specificity of binding. The protein factors in these DNA binding activities were purified using various chromatography techniques. Mass spectrometry analysis of the purified 70 kDa protein corresponding to the 0.33 Rf band activity and a subsequent search in the Dictyostelium genomic database revealed that the purified protein was a putative formyltetrahydrofolate synthase. / Ph. D.

Gene regulation is a critical aspect of normal development, energy conservation, metabolic control, and responses to environmental cues, diseases and pathogens in eukaryotic organisms. In order to appropriately respond to environmental changes and advance through the life cycle, an organism must manage the expression levels of a large number of genes by utilizing available gene regulation mechanisms. The developmental control of 5â -nucleotidase (5nt) expression in the model system Dictyostelium discoideum has provided a focal point for studies of gene regulation at the level of transcription. In order to identify temporally-regulated control elements within the promoter of the 5nt gene, 5â and internal promoter deletions were designed and fused to the luciferase and lacZ reporter genes, and reporter enzyme activity was measured in cells from the slug stage of development. The results from these experiments enabled the identification of a 250 bp region of the promoter, which was used as a template for subsequent site-directed mutagenesis experiments. These experiments involved altering 6-12 bp regions of the promoter by substitution. Twelve mutagenized promoters were fused to the luciferase and lacZ reporter genes, and activity was measured at the slug stage of development to more precisely locate cis-acting temporally-regulated control elements. In addition, cAMP induction experiments were performed on amoebae transformed with the mutagenized promoters to identify control elements within the promoter influenced by the presence of cAMP. The regions between -530 and -560 bp and -440 and -460 bp from the ATG translation start site. In order to evaluate the functions of the cis-acting promoter control elements, electromobility gel shift assays were performed to identify specific DNA-protein interactions on the 5nt promoter. These assays enabled the detection of a 0.13 Rf and 0.33 Rf binding activity to specific sites of the promoter. After characterization of these binding activities, both proteins were purified by a series of column chromatography techniques and characterized after mass spectrometry. The proteins purified were identified as formyltetrahydrofolate synthase and hydroxymethylpterin pyrophosphokinase. These enzymes function in the biosynthetic pathway of tetrahydrofolate and the production of folate coenzymes. The specific interactions of these enzymes with the 5nt promoter suggest these proteins may also function in regulating 5nt expression. / Ph. D.

Regulation of gene expression is known to be a critical factor involved in proper development, responses to environmental cues, metabolism, energy conservation, and disease. Gene expression is regulated at several levels including transcription, mRNA splicing, post translational modification, and the rate of protein degradation. The developmental control of <i>alkaline phosphatase</i> (alp) in <i>Dicytostelium</i> has provided a focal point for the study of gene regulation at the level of <i>de novo</i> synthesis. The localization of <i>alkaline phosphatase</i> (alp) expression during development was characterized by fusing the 5' flanking sequence to the <i>lacZ</i> reporter and using an <i>in situ</i> β-galactosidase staining method. The localization of </i>lacZ</i> expression corresponds with that of the endogenous ALP enzyme suggesting that <i>alp</i> is regulated at the level of transcription. In order to identify temporal regulatory elements within the <i>alp</i> promoter a series of 5' and internal promoter deletions were generated and fused to the <i>lacZ</i> reporter. The data from these promoter deletion constructs indicated a regulatory element within the -683 to -468 bp sequence that is required for normal expression of <i>alp</i> during development. A series of small internal and 5' promoter deletions were designed within the -683 to -468 bp regulatory sequence. The results from these promoter deletion-reporter gene fusions suggested a DNA regulatory element is located within a 26-bp sequence beginning at the -620 bp site. The function of <i>cis</i>-acting regulatory elements were evaluated using the electromobility shift assay (EMSA) to identify sequence specific DNA-protein interactions on the <i>alp promoter</i>. We report the characterization of three DNA-binding activities with the 20% ammonium sulfate (AS) slug nuclear fraction. These DNA-binding activities appear to be related as they all require magnesium or calcium for effective binding to the <i>alp</i> promoter. Interestingly, the DNA-binding proteins appeared to interact with a GT-rich sequence that contained a G-box binding factor (GBF) consensus element. Additionally, a DNA-binding activity observed in the 80% AS slug nuclear extract was characterized and sequentially purified using conventional and affinity chromatography techniques. The DNA-binding protein was identified as TFII, a protein that was previously identified during the investigation of <i>glycogen phosphorylase-2 (gp2)</i> regulation. A comparison of the <i>alp</i> and <i>gp2</i> probes used to identify TFII suggests a DNA-binding site, ACAATGN₈₋₁₂CACTA. The ability of TFII to bind specifically with the promoter of two functionally different genes suggests that it may regulate the temporal and/or spatial expression of several <i>Dictyostelium</i> genes. / Ph. D.

名古屋大学博士学位論文 学位の種類:博士(医療技術学) (課程) 学位授与年月日:平成23年3月25日

Abstract This study was initiated to elucidate the complete genomic structures of type XV collagen in man and mouse and the functional properties of their promoters, as well as to obtain knowledge of the biological role of type XV collagen during development and maturity using immunofluorescence and transgenic techniques. The cloning and characterization of genomic clones revealed that the human COL15A1 gene is 145-kb in size and consists of 42 exons, and the mouse Col15a1 gene is 110-kb with 40 exons. The genomic organization of the two genes was found to be highly conserved, except for two regions of divergence. The nuclease S1 protection analysis revealed multiple transcription initiation sites in both genes, which is in accordance with the overall genomic structures of their 5'-flanking sequences. Transient cell transfection experiments with varying lengths of 5'-deletion constructs identified the fragments necessary for basic promoter activity in both genes and those implicated in the positive and negative regulation of the mouse Col15a1 gene. Furthermore, the involvement of transcription factor Sp1 in the gene regulation of the human COL15A1 gene was demonstrated. A mouse specific polyclonal antibody against type XV collagen was generated and utilized in the localization of type XV collagen protein in developing and mature mouse tissues. Type XV collagen was deposited early in the development and was particularly prominent in capillaries. Spatio-temporal differences in the expression of type XV collagen in various capillary types was demonstrated. Early expression was also detected in the skeletal muscle and peripheral nerves, while expression in the heart, lung, and kidney appeared to be developmentally regulated. Transgenic mice lines expressing truncated type XV collagen driven by either short or long endogenous type XV collagen promoters were generated. The two promoters conferred different tissue-specificities and expression levels, the longer one resulting in more endogenous-like expression. Despite some expression at both mRNA and protein levels, the truncated type XV collagen did not cause any obvious phenotypic or histological changes in any of the lines driven by the shorter promoter fragment. In heterozygote matings of one of the lines driven by the longer promoter fragment, however, a portion of the transgene positive mice appeared to be lost prenatally. Furthermore, pregnancy terminations in this line indicated a high number of abortions beginning at about 11 days of development. Further studies are needed before detailed conclusions on the consequences of the generated mutation can be drawn. The elucidation of the genomic structure of the human COL15A1 gene provides the necessary database for screening mutations in patient samples for candidate diseases caused by this collagen. The genomic clones and the mouse-specific antibody against type XV collagen are valuable tools also in future projects. The knowledge of the developmental dynamics of type XV collagen is of great value, as it helps to understand the physiological consequences that the as yet unidentified mutations in type XV collagen may cause in humans.

Combinatorial control of transcription is a well established phenomenon in the cell. Multiple transcription factors often bind to the same transcriptional control region of a gene and interact with each other to control the expression of the gene. It is thus necessary to consider the joint conservation of sequence pairs in order to identify combinations of binding sites to which the transcription factors bind. Conventional motif finding algorithms fail to address this issue. We propose a novel biclustering algorithm based on random sampling to identify candidate binding site combinations. We establish bounds on the various parameters to the algorithm and study the conditions under which the algorithm is guaranteed to identify candidate binding sites. We analyzed a yeast cell cycle gene expression data set using our algorithm and recovered certain novel combinations of binding sites, besides those already reported in the literature. / Master of Science

名古屋大学博士学位論文 学位の種類:博士（医療技術学） (課程) 学位授与年月日　平成22年3月25日

No description available.